Why don't I see any protein after TEV cleavage?

In the yeast TAP-tagged strains, the problem visualizing the TAP-tagged protein using the anti-TAP antibody after TEV cleavage can be due to interference of the zz domain of Protein A. If you cleave the TAP tag with TEV, without first running the sample on an IgG column, a mixed population will exist of the TAP-tagged protein plus the zz domain of Protein A. Protein A tends to be "sticky" with regard to the binding domain and will react with the anti-TAP antibody thus reducing the signal of your protein of interest on a western blot. To reduce the likelihood of this problem, you will need to run your cleaved sample against immunoglobin beads (i.e. IgG beads) to pull the zz domain of Protein A out. If you are using an IgG column to purify the protein, simply be aware of the stringency of the elution buffer and the potential of the Pprotein A domain partially eluting with your protein. It is a good idea to run a gel after you elute from the column to ensure that you do not have the Protein A domain present. You can blot your protein if necessary.